Clinical Microbiology Laboratory Users Manual November 2019

Public Health Laboratory, Dublin Health Service Executive

Public Health Laboratory Users Manual

Issue No. 007 Issue Date: 08/02/2022 Page 1 of 23

Issued by: Lucy Devlin Approved by: Eleanor McNamara Location(s): Files 5 Appendix and website

U:\Quality System Files\F05. Sample Handling\Users Manual PHL Issue 007.Doc

PUBLIC HEALTH LABORATORY,

DUBLIN

HEALTH SERVICE EXECUTIVE

USERS MANUAL

Issue date: February 2022

Review: February 2023

Public Health Laboratory, Dublin

Health Service Executive,

Cherry Orchard Hospital,

Dublin 10.

Tel: 01 7955175/6

Fax: +353-1-6231908

Email: [email protected]






FOREWORD

The aim of this manual is to aid all users of the Public Health Laboratory, Health

Service Executive, Dublin (PHL, HSE, Dublin) gain the optimum service from the

laboratory appropriate to their needs and public health priority. In particular, it will

aid the user in selecting and obtaining the most appropriate specimen for

microbiological analysis. The user needs to submit the appropriate requestor, patient

unique identifiers and sample information on the relevant PHL HSE Dublin forms for

the optimum test selection. Transporting the appropriate sample to the laboratory

under the correct conditions, packaging and within the acceptable time frames will aid

quality analysis and appropriate interpretation of results. The value of a particular

bacteriology test result is still greatly dependent on these pre-analytical, analytical and

post analytical processes.

Document control:

All changes made to this new issue (Issue 007 of 2022) document are highlighted in

yellow.

Authors: Dr. Eleanor McNamara, Laboratory Director and Consultant

Microbiologist

Lucy Devlin, Quality Manager.






CONTENTS

General Information and scope of PHL, HSE,

Dublin………………………………………………………………………………...5

Data Protection……………………………………………………………………….6

Opening Hours………………………………………………………………………...6

Out of Hours service…………………………………………………………………..6

Clinical Advice………………………………………………………………………..7

User satisfaction…………………………………………………………….…………7

PHL Contact Numbers…………………………………………………….…..............8

Sample Submission …………………………………………………………….……..9

VTEC ……………………..……… ………………… …………......9

Campylobacter samples………………………… ……………………….9

Completion of PHL, HSE Request Forms………… ……….….9

Specimen/Sample Identification………………………… ….…….10

Transport of Clinical Specimens/Samples to the Laboratory…… …….…..10

Food sample Submission………………………………………… …….13

Water sample Submission………………………………………… ………14

Sample Rejection…………………………………………………………………......15

Sample Retention and Further Test Requests………………………………………...15

Complaints Procedure………………………………………………………………..16

Turnaround Time……………………………………………………………………..16

PHL Protocol for Phoning Results………………………………………………...…16

PHL Policy on Faxing and E-mailing Reports……………………………………….17






Summary of National Reference VTEC / Campylobacter/ C. difficile Reference

service and Clinical Microbiology service…………………………………..………18

Summary of the Food Testing Service……………………………………………....20

Summary of the Water Testing Service……………………………………………...20

Appendix 1 Scope of Micro testing at PHL HSE Dublin …..………..………….…21






GENERAL INFORMATION AND SCOPE OF PHL, DUBLIN

This user manual provides information on the activities and structure of the Public

Health Laboratory, Dublin.

The Public Health Laboratory is a Health Service Executive laboratory, located within

the grounds of Cherry Orchard Hospital, Ballyfermot, Dublin 10, and is administered

by HSE Community Healthcare East, CHO 6. It incorporates INAB (Irish National

Accreditation Board) accredited National reference microbiology laboratory services,

regional and local clinical and environment microbiology services and is a designated

Official food testing laboratory (S.I. 79/2020 -EU Official Control of Foods). The

laboratory microbiology scope is for:

1. A National VTEC (verocytotoxin E. coli) Reference Laboratory (NRL-VTEC)

clinical service. Clinical and environmental samples are analysed for VTEC

utilising molecular and culture techniques. The VTEC service is accredited to

ISO 15189 for clinical enteric specimens and ISO 17025 for food, water and

environmental samples.

2. A National sentinel Reference clinical service for Campylobacter

characterisation, which commenced in 2019 and has now been incorporated

into our routine service.

3. A National Clostridioides difficile Reference Laboratory service. (Some parts

of testing methodology are currently unaccredited).

4. A detailed gastro-enteric clinical microbiology diagnostic service (including

bacteria, viruses, ova and parasites) accredited to ISO 15189, for clinical

management, surveillance and to support and advise on the investigation of

gastro-enteric outbreaks both nationally and regionally.

5. An ISO 17025 accredited Regional Public Health food and water

microbiology analytical service. This is accessed by the Environmental Health

Service (EHS), Public Health Doctors and Acute Hospital Facilities.

Clinical samples, bacterial isolates, food and water samples are tested for

microbiological analysis only.

The results of any unaccredited tests are marked by an asterisk.

Clients will be informed of any change to the accreditation status of the Public Health

Laboratory HSE Dublin.

It is the policy of the laboratory not to refer tests within the scope of the laboratory, to

external laboratories. If, in exceptional circumstances, the PHL must subcontract tests

for which it is accredited, PHL would ensure that the work was sent to an accredited

laboratory where possible and clients would be informed.






DATA PROTECTION

The Public Health Laboratory complies with the data protection and confidentiality

policies of the HSE, thus ensuring all data is processed in line with the principles of

the General Data Protection Regulation (GDPR) and relevant Irish legislation.

IMPARTIALITY

The laboratory functions as a distinct entity to carry out a range of services, thus

guaranteeing its impartiality. Staff are required to sign a declaration of impartiality.

The requirement for on-going impartiality is documented.

OPENING HOURS:

The PHL’s routine service is provided from 9.00 a.m. to 5.00 p.m. Monday-Friday. A

limited service is provided on Saturday mornings from 9.30 a.m. to 12.30 pm and

Sundays from 10.00 to 12.00 mid-day. Urgent samples are facilitated outside of these

hours. Please contact the laboratory to arrange the receipt of all urgent specimens in

advance of sending them by contacting Cherry Orchard Hospital (COH) switch. See

‘out of hours’ contact details below or if during working hours, please phone PHL

HSE Dublin at 01-7955174/5 Out of hours, non urgent specimens may be delivered to

the gate lodge of COH and refrigerated overnight until collection by PHL staff.

PHL clerical staff are available for phone queries about validated results or for general

enquiries etc. from 9.00 a.m. to 5 p.m. Monday to Friday at 01 7955175/6.

OUT OF HOURS SERVICE:

A Consultant Microbiologist approved emergency ‘out of hours’ service is available

between 5 p.m. and 9 a.m. Monday to Friday and between 12.30 p.m. on Saturday to

9.00 a.m. on Monday (i.e.7/7). This service is accessed only by contacting the

Laboratory Director or the designated Consultant locum. Their contact details are

available via the Cherry Orchard Hospital switchboard (01 7955000).

Note: The Consultant Microbiologist must be telephoned (via the Cherry Orchard

Hospital switchboard 01 7955000) in advance for approval to analyse urgent

specimens to be processed out of hours. Users should not telephone the laboratory as

telephones are not staffed out of routine hours.






CLINICAL ADVICE: Advice regarding diagnosis and treatment of infection is available at all times.

Contact numbers are given overleaf. For out of hours advice including infection

control advice, please contact the on-call Consultant Microbiologist via switchboard

(01 7955000).

Environmental result interpretation (food and waters)

Advice regarding interpretation of environmental results on the final report is

available at all times. Contact numbers are given overleaf.

USER SATISFACTION:

The Public Health Laboratory operates an on-going process of service evaluation and

improvement to meet the needs and requirements of users. Laboratory management

regularly assesses contributions and complaints received in the laboratory from users

of the Microbiology service. User satisfaction is assessed by either periodical

questionnaires or User open days. Open days are targeted to specific clients.

Please write or email the Chief Medical Scientist or Quality manager






PHL CONTACT NUMBERS (01 7955175)

Name Ext. E mail

General secretarial office

General enquiries/results

01 7955175/6 [email protected]

Consultant Microbiologists

Dr. Eleanor McNamara 01 7955214 [email protected]

Dr. Brian O’Connell 01 7955214 [email protected]

Prof. Johannes Wagner 01 7955214 [email protected]

Chief Medical Scientist

Anne Carroll

01 7955247

[email protected]

National Reference Laboratory(NRL)

Service

Dr. Eleanor McNamara

Anne Carroll

01 7955214

01 7955247

[email protected]

[email protected]

Clinical Laboratory

Senior Medical Scientist

Donal Lanigan

01 7955174

[email protected]

Food Laboratory

Senior Medical Scientist

Aidan Gibson

01 7955216

01 7955249

[email protected]

Water Laboratory

Senior Scientist

Paul Larkin

01 7955217

01 7955250

[email protected]

Quality Manager

Lucy Devlin

01 7955248 [email protected]

Infection Control Nurse Specialist

Triona Mills

01 7955215 [email protected]

mailto:[email protected]

















SAMPLE SUBMISSION

GENERAL GUIDELINES

All samples submitted to PHL should be in the appropriate sterile container

accompanied by the relevant completed PHL Dublin request form (available on

the PHL website). Samples should be transported to the laboratory as soon as

possible under the appropriate transport conditions (see relevant section below).

VTEC, CAMPYLOBACTER, C. DIFFICILE AND CLINICAL SAMPLE

SUBMISSION:

Samples should be submitted with the appropriate accompanying PHL request

form – see PHL website. Collect appropriate clinical specimens in sterile containers

before commencement of antimicrobial therapy if possible. This is usually possible

for most mild infections. For more serious infections, antimicrobial therapy should

not be withheld pending collection of a specific specimen.

If in any doubt as to the appropriate container, please contact the laboratory for

advice.

Please send an adequate amount of specimen. As a general rule – ‘the more specimen

the better’.

COMPLETION OF PHL CLINICAL REQUEST FORMS:

Adequate identification of patient (including at least 2 unique identifiers) samples

is essential for patient safety.

The following details should be recorded on the request form:

Full Patient Name

DOB

Patients Address

External laboratory number/MRN (where available)

Gender

Date of sample Collection

Ward/Source

Requesting Clinician and contact details (all clinical samples must be

requested by a named medical Doctor).

Specimen Type

Tests requested with relevant clinical details.






Those highlighted in bold are mandatory and include patient identifiers.

Please ensure that relevant clinical details are included on the request form. Please

include details if the specimen is associated with an outbreak (provide outbreak code)

investigation, in an ‘at risk’ occupation (Health Care or Food Worker) or if there is a

history of foreign travel, or a specific diagnosis is being considered. All of the above

may influence the type of test that the laboratory performs.

Bacterial isolates for identification, characterisation or toxin testing must be

accompanied by a current VTEC, Campylobacter or C. difficile NRL request form.

All PHL Dublin request forms are available from our website:

https://www.hse.ie/eng/services/list/5/publichealth/publichealthlabs/public-

health-laboratory-dublin/

CLINICAL SPECIMEN/SAMPLE IDENTIFICATION

The following details should be recorded on all specimen containers:

Full Patient Name

DOB

MRN (where available)

Date of collection

Those highlighted in bold are essential patient identifiers.

Specimens cannot be processed unless there is a minimum of two patient identifiers

on the specimen which match those on the request form, one of which must be the full

patient name. If the sample does not have the two patient identifiers or is

unsuitable (i.e. leaking) the sample will be rejected and a repeat sample

requested. The sample is still logged in and is recorded as a rejected sample on

our Laboratory Information Management System (LIMS). The doctor or

hospital laboratory will be phoned to inform them that the sample is not being

processed and repeat testing offered.

It is laboratory policy NOT to process unlabelled or mislabelled specimens.

TRANSPORT OF CLINICAL SPECIMENS/SAMPLES TO THE

LABORATORY.

All samples must be packaged appropriately. It is the responsibility of the person

dispatching the sample to the laboratory to ensure that it is packaged correctly and

https://www.hse.ie/eng/services/list/5/publichealth/publichealthlabs/public-health-laboratory-dublin/

https://www.hse.ie/eng/services/list/5/publichealth/publichealthlabs/public-health-laboratory-dublin/






does not pose a risk to anyone coming in contact with it during transport or on

receipt in the laboratory (Ref: S.I. No.617 of 2010 Carriage of Dangerous Goods

by Road Regulations 2010).

Specimens should be transported and processed as soon as possible; individual test

requirements may invalidate the test request if the samples is too old (48-72h).

All Category B biological substances should be packaged according to UN3373 IATA

Packaging Instruction 620. Clinical samples should be put into a small plastic specimen

bag with enough absorbent material to soak up the entire sample if a leak occurs.

Isolates should be on a suitable growth medium (e.g. Nutrient Agar slope) and sealed

with Parafilm beforehand.

The Primary container is then placed into a secondary screw top plastic container.

The secondary container should be certified leak proof at 95KPa and filled with paper

towel or cotton wool so that the specimen is secure and does not rattle in the container.

The Secondary container is put into a Category B labelled cardboard box which has an

address label, UN3373 label and orientation label.

Faeces samples are held at room temperature if they are to be processed on the day of

arrival in the laboratory. Other sample types are refrigerated at 2 - 8º C.

If processing is delayed sample should be refrigerated at 2 - 8º C for a maximum of 72

hours.

Urgent samples will be processed upon receipt or discussed with Consultant

Microbiologist if received out of hours. Clients sending urgent samples should notify

the laboratory in advance as outlined above.

1-2g is sufficient for culture of faeces. As multiple samples are rarely indicated for

detection of faecal pathogens, if more than one sample is taken on the same day they

may be pooled.

Isolates received for VTEC analysis before 11a.m. will be processed directly from the

slope/plate on the day of receipt.

For ova and parasite analysis, ideally three stool samples should be collected over no

more than a 10-day period. It is usually recommended that samples are collected every

other day. Unless the patient has severe diarrhoea or dysentery, no more than one

sample should be examined within a single 24 hour period, as shedding of cysts and

ova tends to be intermittent. If E. histolytica or G. duodenalis are suspected and the

first 3 samples are negative, ideally 3 additional samples should be submitted at weekly

intervals. There are no prescribed limits for the size of sample required, but some

laboratory procedures will require larger quantities than others.

For Sellotape slides/perianal swabs suspecting E. vermicularis ova, the sample should

be taken between 10pm and midnight, or early in the morning, before defecation or

bathing. To prevent deterioration, refrigeration or storage of sample at room

temperature for up to 48hrs is advised. It is recommended that samples should be taken

for at least 4 to 6 consecutive days. If the results of all these are negative the patient






can be considered free from infection. In practice, more than one sample is rarely

received.

Samples requesting detection of S. haematobium, it is preferable to obtain total urine

collected over the time period between 10am and 2pm. A minimum of 10ml is

required. In patients with haematuria, eggs may be found trapped in the blood and

mucus in the terminal portion of the urine sample. If the urine cannot be examined

within an hour of collection, it is advisable to add 1mL of undiluted formalin to

preserve any eggs that may be present. For duodenal/jejunal aspirates, a minimum

volume of 1mL is required.

Fresh faeces samples are essential for the examination of trophozoites ideally within 30

minutes from the time of collection.

SWABS/CONTAINERS USED IN THE PHL HSE, DUBLIN

1. Universal container – two types with different apertures are used for collection of

bodily fluids.

2. Amies Transport swabs for routine collection of rectal swabs.

If you have any other queries, please contact the laboratory.






FOOD AND WATER SAMPLE SUBMISSION:

FOOD SAMPLES:

Foods should be sampled and transported to the laboratory as per “FSAI/HSE

Guidance on Sampling of Food for Microbiological Testing (Current Issue)

Official Food Sample

Under the terms of the Official Control of foodstuffs Directive 93/99/EEC and

EU 2017/625 an official food sample must be examined in an official Food

Control Laboratory. The Public Health Laboratory is designated as an official

food testing laboratory under S.I.79 of 2020. Official food samples should

have a documented chain of custody as all food sample results are legally

actionable and all food results are copied to the Food Safety Authority of

Ireland as the competent Authority.

Specimen Request Form for Food samples.

A specimen request form (National Sample Submission Form (NSSF)) should

accompany each sample of food to be tested. The receiving PHL staff member must

record the following details on the requisition form:

1. Date and time of receipt of sample.

2. Temperature of sample on receipt if appropriate

3. Receivers name

4. Storage condition on receipt

5. Tick box once sample and form information has been crosschecked.

By the EHO:

1. Name of the EHO delivering sample

2. Name of EHO collecting sample

3. Food type and code

4. Packaging conditions etc

5. Reason for sampling

6. Supplementary information if food poisoning outbreak

7. Premises name and sample description.

8. Any other comments about the sample

Sample Size

The standard minimum routine food sample size in a sterile container for the PHL is

100g (25g x 4). This may vary depending on sample availability, for example, if the

sample is related to a complaint.






WATER SAMPLES:

Water samples must be submitted in sterile containers. The sample container must

contain sodium thiosulphate if the water sample has been treated with a biocide (e.g.

chlorine).

If in any doubt as to the appropriate container or transport conditions, please contact

the laboratory for advice.

Specimen Request Form for Water samples

A PHL Dublin request form should accompany each sample of water sample to be

tested. The receiving PHL staff member will record the temperature of the container

that was used to transport the sample.

See Table 1 for the minimum volume of sample required and the type of container

required.

TABLE 1

Sample type Min. Vol. required Sodium

Thiosulphate

Sterile

Container

Mains/ Drinking Water 500ml Required YES

Endoscopy water 500ml Required(If

biocide)

YES

Heater cooler water 300ml Required(If

biocide)

YES

Swimming Pools 500ml Required YES

Hydrotherapy pools 500ml Required YES

Well Water

(microbiologically treated)

500ml Required(If

biocide)

YES

Well water untreated 500ml Not Required YES

Group Scheme (treated) 500ml Required(If

biocide)

YES

Group Scheme (untreated) 500ml Not Required YES

Seawater 500ml/1000ml/2000ml Not Required YES

Surface water 500ml Not Required YES

Water for pathogens

(eg. VTEC, Salmonella,

Campylobacter)

At least 1 litre If biocide present YES






Bottled water At least 1 litre YES

Pre bottled water At least 1 litre If biocide present YES

Water for dialysis 500ml If biocide present YES

Water for Legionella

testing

At least 1 litre YES

Please ensure that relevant details are included on the request form. All of the above

may influence the type of tests that the laboratory performs.

The current PHL Dublin food and water sample request forms are available to

download from the website:

https://www.hse.ie/eng/services/list/5/publichealth/publichealthlabs/public-

health-laboratory-dublin/request-forms.html

SAMPLE REJECTION:

Referred samples that don’t meet the required acceptance criteria will be registered

and discussed with a Senior Scientist or Consultant staff. If the decision is to reject

the sample, it will be discarded and the reason for rejection noted and informed to the

referring doctor/laboratory/environmental health officer. It is laboratory policy NOT

to process unlabelled or mislabelled samples. Where deviating samples are chosen to

be processed, this will be recorded as such and, if applicable, an interpretation will be

applied cautiously.

SAMPLE RETENTION AND ADDITIONAL TESTING REQUESTS:

Clinical Specimens:

Following testing, routine clinical samples are stored at 2 - 8º C for a week or until the

final report has been authorised.

Samples processed in the CL3 laboratory are stored at 2 - 8º C for a minimum of a

week.

Requests for additional testing on samples may be possible on a case-by-case basis,

once agreed by PHL HSE Dublin staff up to 72 hours after receipt. Please contact the

laboratory as soon as possible if the need for additional testing is identified. If a

client/user requests additional testing verbally, it must be followed up by a written

confirmation.

If there is a delay in processing a sample, that could compromise patient care, then

the requestor will be informed of this by PHL.

https://www.hse.ie/eng/services/list/5/publichealth/publichealthlabs/public-health-laboratory-dublin/request-forms.html

https://www.hse.ie/eng/services/list/5/publichealth/publichealthlabs/public-health-laboratory-dublin/request-forms.html






Food and Water Samples;

Where practicable, food samples are frozen at -20ºC on the day of testing and retained

in the laboratory for up to three weeks.

Water samples are stored in the fridge for up to a week. A sample will be held for

longer than a week should further testing be required and/or until the final confirmed

results are obtained.

VTEC, Campylobacter and C. difficile Isolates:

VTEC and Campylobacter isolates are logged with unique identifiers and stored

indefinitely on freezer beads at -70ºC.

COMPLAINTS PROCEDURE:

A complaints procedure is in place in the Public Health Laboratory. Initial complaints

may be received and documented by phone, email or letter.

All complaints will be fully investigated in accordance with our quality management

system documented protocols (See PHL HSE Dublin Quality Manual and File 8).

TURNAROUND TIMES:

Turnaround times vary depending on the sample type and the tests requested, and is

the maximum number of days between sample receipt and issue of result.

When sending a culture to PHL for VTEC testing, please pick from a non-selective

medium or check the purity of the isolate before sending. Submitting a pure culture

ensures that VTEC PCR results are available within 24 hours. The turnaround time for

VTEC isolates is 4 working days.

The turnaround time for VTEC and/or routine stools is 6 working days.

The turnaround time for routine Campylobacter requests for confirmation and

phenotypic antimicrobial sensitivity results is 6 working days.

The turnaround time for NRL Campylobacter samples is 6 working days.

The turnaround time for NRL C. difficile samples is 6 working days.

The turnaround time for enteric viral PCR screen is 3 working days.

The turnaround time for whole genome sequencing on isolated bacteria is generally

two weeks. However, during outbreaks periods of heavy workloads, this will be

longer for routine isolates as urgent outbreak isolates will be prioritised.

Faeces/Duodenal Aspirates

Turnaround times for Ova and Parasites - microscopy and/or PCR result within 3

working days. If a sample is for routine culture or VTEC studies as well as O/P, it






may take up to 6 working days before the result is reported. Any positive parasites

will be phoned straight away.

Sellotape Slide/Perianal Swab

Written report within 72hrs

PHL PROTOCOL FOR PHONING RESULTS:

Clinical results

All preliminary positive results, of clinical significance are phoned within 24 hrs to

the relevant requesting Doctor (i.e. the requesting medical doctor-GP or relevant

Public Health doctor). Positive results of samples, received from clinical laboratories,

are phoned to the requesting laboratory scientific staff or medical personnel. Such

phone calls are documented on LIMS and the final report/cert. of analysis

Environmental results

If a significant pathogen is detected, a preliminary result will be phoned to the

Environmental Health Officer or laboratory Scientist and then a final hard copy result

dispatched. Such phone calls are documented on LIMS and the final report/cert of

analysis.

PHL POLICY ON FAXING AND E-MAILING REPORTS:

The public health laboratory complies with the Health Service Executive’s policies on

electronic transmission of results.






A. SUMMARY OF NRL VTEC, CAMPYLOBACTER AND C. DIFFICILE

SERVICE AND CLINICAL MICROBIOLOGY SERVICE:

The PHL provides a National VTEC Reference service for clinical samples. We also

provide a sentinel National Reference service for Campylobacter characterisation, and

we were awarded the tender to provide a C. difficile National Reference Service in

2021. These services are accessed by Directors/ Clinical Microbiologists/ Chief

Medical Scientists of regional and primary clinical laboratories, and Public Health

Doctors, who submit samples or presumptive isolates for confirmatory VTEC,

Campylobacter and C. difficile studies and detailed molecular strain characterisation.

The Environmental Health Service send environmental samples for VTEC analysis.

Verocytotoxin producing E. coli (VTEC), Campylobacter and C. difficile isolates

The range of services includes:

Identification to genus and species level

Phenotypic and molecular typing.

Whole genome sequencing for antimicrobial resistance determinants,

virulence factors and cluster analysis of potential public health significance.

This is novel methodology is currently not accredited.

The following are some recommended samples to be sent from patients with

particular clinical syndromes -

GASTROINTESTINAL TRACT INFECTION

Gastroenteritis

Please note that this laboratory employs a cost-effective approach to the diagnosis of

infectious diarrhoea. Not all specimens are examined for every pathogen. It is

therefore important that clinical details or suspected diagnoses are included on the

request form. Information that is of use when processing specimens includes: travel

history, occupation, relationship to a particular food, prolonged diarrhoea, antibiotic

use, suspected outbreak. The laboratory examines stool samples routinely for:

Salmonella sp.

Shigella sp.

VTEC (Verotoxigenic E. coli)

Campylobacter sp.

Clostridium difficile toxin detection by PCR and culture of PCR positive

samples is performed on all specimens from patients over 2 years of age.






Samples are tested using molecular methods for the above pathogens and all

PCR positive samples are further tested by culture methods in order to isolate

the organism if possible.

Other pathogens e.g. Yersinia, Vibrio, Aeromonas, enteric viruses, ova and

parasites (O/P) etc. are only examined if the clinical details suggest that

possibility or if specifically requested.

An O/P PCR method is used for Cryptosporidium, Giardia, Entaomoeba

Histolytica and Dientamoeba fragilis. Traditional wet prep O/P microscopy is

also available.

Ova and Parasite testing may be requested if the patient has had chronic

unexplained diarrhoea, if the patient is immunocompromised or if there is a

history of foreign travel.

Rotavirus/Adenovirus PCR stool detection is performed on patients under 5

years of age.

Norovirus and other enteric viruses (adenovirus, sapovirus, enterovirus,

rotavirus) PCR stool detection is available when clinically indicated.

When to send a stool specimen: Send a stool specimen to the laboratory when there

are ≥3 liquid or very loose stools (ie. stool takes up the shape of the container) per

day. There may be other symptoms suggestive of infectious diarrhoea e.g. abdominal

pain or discomfort, nausea, faecal urgency, tenesmus, fever, blood or mucus in stools.

Asymptomatic patients may be requested to submit stool samples in outbreak

investigations. Hospital specimens should be sent to the laboratory immediately. In

General Practice, please refrigerate stools if there is to be a delay in transporting the

specimen.

How much stool to send: Please fill the specimen container to between ¼ and ½ full.

Please do not fill to the brim.

RECTAL SWABS

Rectal swabs are used to detect enteric carriage of multi drug resistant organism’s

(MDRO’s) e.g. vancomycin resistant Enterococci (VRE) or carbapenem producing

Enterobacteriaceae (CPE). The tip of a sterile swab is passed approximately 2.5 cm

beyond the anal sphincter. Rotate the swab gently and withdraw it and place the swab

into the container with the appropriate transport medium.






B. A SUMMARY OF THE FOOD TESTING SERVICE:

The Public Health Laboratory is designated an “Official Laboratory” approved for

Microbiological testing under Statutory Instrument (SI) 79/2020: European

Communities (Official Control of Foodstuffs) Regulations 2020.

ISO 17025 ACCREDITATION:

The Public Health Laboratory is accredited to ISO 17025 by the Irish National

Accreditation Board. ISO 17025 section 6.6 requires laboratories to review the

competency of referral laboratories. A competent referral laboratory is one that

complies with this International Standard.

For information:

The current scope of accreditation for the PHL, HSE Dublin Laboratory is freely

available as a “pdf” download from the INAB web site at:

https://www.inab.ie/fileupload/testing/public-health-laboratory-dublin-101t.pdf

Food samples are tested for a comprehensive microbiological scope in accordance

with the FSAI/HSE service contract. In addition a significant food safety surveillance

programme of food samples from hospitals is undertaken. Environmental swabs

procured from food business operators are also processed.

A schedule of testing is agreed locally on an annual basis with the environmental

health service (EHS) and hospital catering managers. National surveys are agreed

annually with the Food Safety Authority of Ireland (FSAI).

See Appendix 1 for the list of accredited microbiological food tests available.

C. A SUMMARY OF THE WATER TESTING SERVICE.

A comprehensive accredited microbiological surveillance of many types of waters is

undertaken annually. This includes potable, bottled, therapeutic (Endoscopy, dialysis),

bathing and seawaters. A local schedule of water testing is reviewed and agreed

annually with the HSE, EHS and hospital clients.

See Appendix 1 for the list of accredited microbiological water tests available.

https://www.inab.ie/fileupload/testing/public-health-laboratory-dublin-101t.pdf






APPENDIX 1 SCOPE OF MICROBIOLOGICAL TESTING AT PHL, DUBLIN

Food Tests

PHL Test

number

Test name Primary Reference Accredited

Yes/No

SFM001 Aerobic Colony Count ISO 4833-2:2013 Yes

SFM002 Enumeration of Escherichia coli ISO 16649-2:2001 Yes SFM003 Enumeration of Staphylococcus aureus ISO 6888-1:2021 Yes SFM004 Enumeration of Bacillus cereus including

Bacillus species

ISO 7932:2005 AMD

2020

Yes

SFM005 Enumeration of Clostridium perfringens ISO 7937:2004 Yes SFM006 Detection of Salmonella species ISO 6579-1:2017 Yes SFM007(E) Enumeration of Listeria monocytogenes

and other Listeria species

ISO 11290-2:2017 Yes

SFM007(D) Detection of Listeria monocytogenes and

other Listeria species

ISO11290-1:2017 Yes

SFM008 Detection of Campylobacter species ISO 10272_1:2017 Yes SFM009 Enumeration of Enterobacteriaecae ISO 21528-2:2017 Yes SFM011 Detection of Escherichia coli O157 using

immunomagnetic separation

ISO 16654:2001

AMD 1:2017

Yes

SFM022 Detection of Escherichia coli O26 using

immunomagnetic separation

ISO 16654:2001

AMD 1:2017

Yes

SMM006

Molecular

Detection of Salmonella species in food

samples by DNA extraction PCR

ISO 13136:2012 Yes

Environmental swab tests

SEM001 Detection of Pseudomonas aeruginosa on

environmental swabs

ISO 18593:2004

ISO 16266:2008

Yes

Water Tests

PHL Test

number

Test name Primary Reference Accredited

Yes/No

WSOP 1 General Techniques for the Detection of

Bacteria by Membrane Filtration

ISO 8199:2018 Yes

SWM001 Enumeration of Coliform Bacteria and E

coli by Membrane Filtration

ISO 9308-1:2014

Amendment 1:2016

Yes

SWM003 Enumeration and confirmation of

Enterococci

ISO 7899-2:2000 Yes

SWM004 Enumeration and confirmation of

Clostridium perfringens

ISO 14189:2013 Yes

SWM005 Detection of Salmonella spp. by culture ISO 19250:2010 Yes SWM006 Enumeration of Total Plate Counts 22ºC ISO 6222:1999 Yes SWM007 Enumeration of Total Plate Counts 37ºC ISO 6222:1999 Yes SWM008 Enumeration and confirmation of Ps. ISO 16266:2006 Yes






aeruginosa

SWM009 Detection and enumeration of Coliform

Bacteria and E. coli by IDEXX

Quantitray™

ISO 9308-2:2012 Yes

SWM010 Detection of E coli O157 Using

Immunomagnetic Separation

MDW Part 4:2016 Yes

SWM0012 Detection and enumeration of Legionella

species by membrane filtration

ISO 11731:2017 Yes

SWM0017 Total Viable Count for

Environmental/Endoscopy water

ISO 15883-4 :2018 Yes

SWM0018 Detection of Mycobacterium species by

membrane filtration

ISO 15883-4:2018 Yes

SWM0018M Detection of slow-growing

Mycobacterium spp. from waters from

heater-cooler units

ISO 15883-4:2018 Yes

SWM0019 Enumeration of S. aureus by Membrane

Filtration

HPA W10 No

SWM0020 Detection of E. coli O26 Using

Immunomagnetic Separation

MDW Part 4:2016 Yes

SWM0023 Total Viable Count/ml for Dialysis

waters

ISO 23500:2014

ISO 13959:2014

ISO 11663: 2014

Yes

SMM007

Molecular

Detection of Salmonella spp in water

samples using automated DNA

extraction and real-Time PCR

ISO 13136:2012 Yes

Clinical tests

PHL Test

number

Test name Accredited

Yes/No

SCM001 Investigation of faecal specimens for faecal

pathogens

Yes

SCM002 Investigation of faecal specimens for the detection

and isolation of verotoxigenic E. coli (VTEC) and

enteropathogenic E. coli (EPEC)

Yes

SCM003 Investigation of Ova and Parasites in specimens other

than blood

Yes

SCM004 Antimicrobial Susceptibility Testing Yes






Molecular Tests

PHL Test

number

Test name Accredited

Yes/No

SMM001 Detection of vt1, vt2, vt2f, E. coli serogroups O157,

O26, O104, O145, O111 and O103 by PCR from

bacterial isolates.

Yes

SMM002 Detection of VTEC in food using automated DNA

extraction and Real-Time PCR Yes

SMM003 Detection of VTEC in water using automated DNA

and Real-Time PCR. Yes

SMM004 Detection of VTEC from faecal specimens using

automated DNA extraction and Real-Time PCR

Yes

SMM005 Detection of enteric pathogens using automated

DNA extraction and Real-time PCR

Yes

SMM008 WGS VTEC No

SMM008 WGS Campylobacter No

SMM008 WGS C. difficile No

SMM009 SARS- CoV-2 No

Documents

Clinical Microbiology Laboratory Users Manual November 2019